DeepChek® Whole Genome SARS-CoV-2 Genotyping

The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping is a RT-PCR Assay (nucleic acid technique (NAT)) followed by Next Generation Sequencing (NGS) intended to aid clinical applications and for use on previously diagnosed COVID-19 patients.

Intended Use (CE-IVD) — REF 159A48

The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 is intended to be used for amplifying whole-genome of severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2) in upper respiratory specimens (such as nasal, mid-turbinate, nasopharyngeal, and oropharyngeal swab specimens, and nasopharyngeal wash/aspirate or nasal aspirate specimens) from individuals already tested positive to SARS-CoV-2.
The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 aims to identify SARS-CoV-2 infection by a variant (or lineage) which might aid in clinical applications.

This nucleic amplification test is indicated for use on previously diagnosed COVID-19 patients ONLY. This test is NOT intended to be used as a screening or confirmation test for the detection, confirmation or quantification in upper respiratory specimens of SARS-CoV-2.

Methodology

Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) and Next Generation Sequencing.

The Assay targets and amplify the whole genome (>99%) of SARS-CoV-2 virus, including regions that harbor mutations of interest described as sufficient in databases like Pangolin and Nextclade, including: UK, Indian, South African, Brazilian variants of concern (VOC).

Intended user

The DeepChek® Assay Whole Genome SARS-CoV-2 Genotyping V1 is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of PCR, next generation sequencing workflow and in vitro diagnostic procedures. The current laboratory biosafety guidance for the 2019 novel coronavirus (SARS-CoV-2) shall be followed.

Post PCR – Complementary information

Next Generation Sequencing

The main volume of the product output is then used for next generation sequencing (NGS). The NGS workflow can be
different as the NGS technics and NGS analyzers vary. NGS sequencing instruments are general laboratory use devices.
Sequencing and library preparations reagents are general laboratory use products.
While the validation studies, we used the Illumina iSeq 100 Sequencing System (#20021532) and the following combination
of reagents: ABL DeepChek® NGS Library preparation (catalog #116AX, 24 or 48 or 96 tests), ABL DeepChek® Assay Adapters (catalog #124AX, 1-24, 1-48 or 1-96) and Illumina iSeq 100 Reagent (catalog # 20021533, 300 cycles).
Note: The external clinical study was conducted with Illumina MiSeq NGS analyzer and related MiSeq Reagent Kit, v2 (catalog # MS-102-2003, 500 cycles) with no need to perform the fragmentation step with the ABL DeepChek® NGS Library preparation (catalog #116AX, 24 or 48 or 96 tests).

Downstream NGS Analysis Software

The sequencing raw data are then uploaded in a specific downstream software tailored for SARS-CoV-2 whole genome analysis and interpretation. This software is a standalone medical device. The software itself can be CE-IVD marked and shall rely on recognized and updated public sources about SARS-CoV-2 circulating strains and SARS-CoV-2 lineage definitions and latest knowledge about the clinical impact of genomic variations.
For the validation studies and the external clinical validation study, the next generation sequencing raw data , outputs from Illumina iSeq100 and MiSeq NGS analyzers, were uploaded in a specific downstream software tailored for SARS-CoV-2 analysis which is a standalone medical device: ABL DeepChek® -CoV-2 software (RUO) (licence and module (catalog #S-12-023 (CVL) and #S-12-023 (CVM)).

The DeepChek® Whole Genome SARS-CoV-2 Genotyping Assay can be part of a laboratory validated environment for an end-to-end solution including laboratory automation (liquid handling robot) and laboratory information system integration with the laboratory information system (LIS).

More information on the DeepCheck® SARS CoV-2 Whole Genome – Click here

CE marking only valid for EEA and territories recognizing it – Otherwise it is for RUO application.